BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0003.0004.p (497 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313053|ref|YP_003777145.1| gluconate 2-dehydrogenase [Herb... 760 0.0 gi|300311001|ref|YP_003775093.1| cytochrome c subunit II protein... 352 4e-98 gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-de... 285 4e-78 gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein ... 280 2e-76 gi|300313762|ref|YP_003777854.1| cytochrome c precursor protein ... 247 2e-66 >gi|300313053|ref|YP_003777145.1| gluconate 2-dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 499 Score = 760 bits (1963), Expect = 0.0, Method: Compositional matrix adjust. Identities = 379/451 (84%), Positives = 409/451 (90%), Gaps = 3/451 (0%) Query: 47 LIERGRYLAVASDCIACHTAPRGKPMAGGLAIASPVGEIIATNITPSKSHGIGNYSEAQF 106 LIERG YLA+ASDCIACHTAPRGKPMAGGLAIASPVGEIIATNITPSK+HGIGNY+E QF Sbjct: 52 LIERGHYLAIASDCIACHTAPRGKPMAGGLAIASPVGEIIATNITPSKTHGIGNYTEEQF 111 Query: 107 AAALRRGVRADGANLYPAMPYTAYAALNDADVHALYAYFMKGVAPVDTPTRETALPFPMN 166 AAALRRGVRADGANLYPAMPYTAYAAL+DADV ALYAYFMKGVAPVD TR T LPFPMN Sbjct: 112 AAALRRGVRADGANLYPAMPYTAYAALSDADVQALYAYFMKGVAPVDVATRPTDLPFPMN 171 Query: 167 IRASMKVWNALFLKDQPLAPAPQRSAQWLRGRYLAEGPAHCSSCHTPRGFLMQEKTNLAL 226 +R SMK WNALFLK+QPL P PQRSAQWLRGRYLAEGPAHCS+CHTPRG+LMQEK +L L Sbjct: 172 LRWSMKAWNALFLKEQPLPPQPQRSAQWLRGRYLAEGPAHCSTCHTPRGWLMQEKPDLQL 231 Query: 227 SGAQVGPWYAPNITPHPTAGIGTWSQDELVAYLKTGRVEGRAQAAGSMAEAITHSFSKLT 286 +GAQVGPWYAPNIT HP+AGIG+WSQD+LVAYL+TGR+EGRAQAAGSMAEAITHSFS+LT Sbjct: 232 AGAQVGPWYAPNITSHPSAGIGSWSQDDLVAYLRTGRLEGRAQAAGSMAEAITHSFSRLT 291 Query: 287 DEDLRAIAVYLKETPAIGPDSSTPPTLGTRFEQGKAGNALAQFRGRTLAADSPEEIRGAR 346 +EDLRAIAVY+K+ PAI + G+RF+QGKAGNALAQFRGRTL+A+SPEEIRGAR Sbjct: 292 EEDLRAIAVYIKDRPAIATGDAQGS--GSRFDQGKAGNALAQFRGRTLSAESPEEIRGAR 349 Query: 347 LFSASCASCHGYNGQGTRDGYYPSLFHNSATAGVNANNLIATILYGVERETEDGGHVFMP 406 +FSASCASCHGYNGQG+RDGYYPSLF NSATAGVNANNLIATILYGV+RETE GGHVFMP Sbjct: 350 IFSASCASCHGYNGQGSRDGYYPSLFRNSATAGVNANNLIATILYGVDRETEQGGHVFMP 409 Query: 407 PFGDQPNALNKLSNEDVAALSNYLLKYYGNPDLKVKPEDVAVIRQGGPRSPLLLVARIGM 466 PFGDQPNALNKLSN DVAALSNYLLKYYG P VK EDV VIRQGGPRSPLLL+ARIGM Sbjct: 410 PFGDQPNALNKLSNADVAALSNYLLKYYGKPAATVKAEDVEVIRQGGPRSPLLLMARIGM 469 Query: 467 GVGAVVVVLLLLLGALMVLRRKRIDPEHDWK 497 AV V++LLLL LMV RKR DPEHDWK Sbjct: 470 -GVAVAVLVLLLLVGLMVALRKRPDPEHDWK 499 >gi|300311001|ref|YP_003775093.1| cytochrome c subunit II protein [Herbaspirillum seropedicae SmR1] Length = 453 Score = 352 bits (903), Expect = 4e-98, Method: Compositional matrix adjust. Identities = 205/424 (48%), Positives = 250/424 (58%), Gaps = 24/424 (5%) Query: 44 EAALIERGRYLAVASDCIACHTAPRGKPMAGGLAIASPVGEIIATNITPSKSHGIGNYSE 103 E LI+RG YLA+A DC ACH+ P +GG I+SP+G I +TNITPSK+ GIG+Y+ Sbjct: 29 EGQLIKRGEYLAIAGDCAACHSQKGRAPFSGGHPISSPLGTIYSTNITPSKTAGIGSYTR 88 Query: 104 AQFAAALRRGVRADGANLYPAMPYTAYAALNDADVHALYAYFMKGVAPVDTPTRETALPF 163 QFAAALR+GVRADG+ LYPAMPYTAYA LND DV ALY YFM+GVA VD T LPF Sbjct: 89 DQFAAALRQGVRADGSQLYPAMPYTAYARLNDEDVTALYTYFMQGVAAVDQAAPATDLPF 148 Query: 164 PMNIRASMKVWNALFLKDQPLAPAPQRSAQWLRGRYLAEGPAHCSSCHTPRGFLMQEKTN 223 P NIR SMK WN LFL +P P P +SAQW RG YL +G AHCS+CHTPR FLM E+ Sbjct: 149 PFNIRLSMKAWNWLFLDKKPFEPDPSQSAQWNRGAYLVQGLAHCSTCHTPRNFLMAEQLE 208 Query: 224 LALSGAQVGPWYAPNITPHPTAGIGTWSQDELVAYLKTGRVEGRAQAAGSMAEAITHSFS 283 L G +G WYAP+ITP W+++ L YL +G A AAG M EAI SFS Sbjct: 209 RRLQGGSLGTWYAPDITPAALQAKPAWTREMLADYLASGHAANGATAAGPMLEAIEMSFS 268 Query: 284 KLTDEDLRAIAVY-LKETPAIGPDSSTPPTLGTRFEQGKAGNALAQFRGRTLAADSPEEI 342 +L EDL A+A Y L T A + P G QG + LAA SP Sbjct: 269 RLRREDLEAMASYLLPPTAATAAPAVNKPPAGLTPVQGDD-------TPQALAALSP--- 318 Query: 343 RGARLFSASCASCHGYNGQGTRDGYYPSLFHNSATAGVNANNLIATILYGVERETEDGGH 402 GAR++ +CASCH GQG P L + N +N++ IL GV E G Sbjct: 319 -GARVYMNNCASCHNTAGQGLNG--LPPLQSHPVLRQPNGDNVVMAILEGVLPEHGQGMI 375 Query: 403 VFMPPFGDQPNALNKLSNEDVAALSNYLLKYYGNPDLKVKPEDVAVIRQGGPRSPLLLVA 462 F + L++E VAA++NYLL+ G + V + VA +R GG SPLL +A Sbjct: 376 GFA----------HTLNDEQVAAVTNYLLQDIGGSKVSVTTQRVATLRAGGAASPLLWLA 425 Query: 463 RIGM 466 R GM Sbjct: 426 RAGM 429 >gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-dehydrogenase cytochrome c subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 285 bits (730), Expect = 4e-78, Method: Compositional matrix adjust. Identities = 177/414 (42%), Positives = 232/414 (56%), Gaps = 34/414 (8%) Query: 47 LIERGRYLAVASDCIACHTAPRGKP-MAGGLAIASPVGEIIATNITPSKSHGIGNYSEAQ 105 L+ RG+YLA A DC+ACH+A GKP +GGLAI S G I +TNITP K HGIGNYSEAQ Sbjct: 31 LVARGQYLARAGDCMACHSAA-GKPAYSGGLAIDSGHGIIYSTNITPDKEHGIGNYSEAQ 89 Query: 106 FAAALRRGVRADGANLYPAMPYTAYAALNDADVHALYAYFMKGVAPVDTPTRETALPFPM 165 F+AA+R GVRADG LYPAMPY +YA ++D D+HALY YFM+GV PV + +++ FP Sbjct: 90 FSAAVRHGVRADGTQLYPAMPYPSYAKVSDEDIHALYTYFMQGVQPVASTPPASSMSFPF 149 Query: 166 NIRASMKVWNALFLKDQPLAPAPQRSAQWLRGRYLAEGPAHCSSCHTPRGFLMQEKTNLA 225 NIR MK+WN F D+P SA+ RG YL EG HC SCHTPRG M EK + + Sbjct: 150 NIRWGMKLWNVFFANDKPFREQDGWSAEIKRGAYLVEGLGHCGSCHTPRGVAMNEKASDS 209 Query: 226 -----LSGAQVGPWYAPNITPHPTAGIGTWSQDELVAYLKTGRVEGRAQAAGSMAEAITH 280 LSG + W P++ G+ WS ++V YL+TGR + A AG M+ + H Sbjct: 210 SQAQFLSGGDLNGWAVPSLR-----GMPHWSAQDIVDYLQTGRNK-TASVAGEMSLVVEH 263 Query: 281 SFSKLTDEDLRAIAVYLKETPAIGPDSSTPPTLGTRFEQGKAGNALAQFRGRTLAADSPE 340 S S L EDL+A+A YLK + S G QG A T A D Sbjct: 264 STSHLKREDLQAMAAYLKTLSPVASSGS-----GRVIPQG----VDATVSKLTAAKDL-- 312 Query: 341 EIRGARLFSASCASCHGYNGQGTRDGYYPSLFHNSATAGVNANNLIATILYGVER-ETED 399 G RL+ +CA+CH G+G G +P L + N + L+ IL G TE Sbjct: 313 -TLGERLYLDNCAACHFVTGRGA-PGIFPVLDGATVVNAENPSALLHVILAGARTPSTEK 370 Query: 400 GGHVF-MPPFGDQPNALNKLSNEDVAALSNYLLKYYGNPDLKVKPEDVAVIRQG 452 + MP F ++LS+E+ AAL+ ++ + +GN KV +V +R G Sbjct: 371 APSILVMPGFA------HRLSDEEAAALATFVRQGWGNHAGKVSEREVGKLRAG 418 >gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein [Herbaspirillum seropedicae SmR1] Length = 441 Score = 280 bits (717), Expect = 2e-76, Method: Compositional matrix adjust. Identities = 173/433 (39%), Positives = 239/433 (55%), Gaps = 55/433 (12%) Query: 42 SPEAALIERGRYLAVASDCIACHTAPRGKPMAGGLAIASPVGEIIATNITPSKSHGIGNY 101 S + L++RG YLA A DC+ACHTA GKP AGGLAIA+P+G + ++NITP K +GIGNY Sbjct: 31 SADQQLVQRGEYLAKAGDCVACHTAKGGKPFAGGLAIATPIGTVYSSNITPDKENGIGNY 90 Query: 102 SEAQFAAALRRGVRADGANLYPAMPYTAYAALNDADVHALYAYFMKGVAPVDTPTRETAL 161 SE F ALR G+R DGA+LYPAMPY +YA + ADV ALYAYFM GV P R + Sbjct: 91 SEEDFDRALRHGIRKDGASLYPAMPYPSYAKVKPADVKALYAYFMHGVQADPAPNRGVDI 150 Query: 162 PFPMNIRASMKVWNALFLKDQPLAPA-----PQRSAQWLRGRYLAEGPAHCSSCHTPRGF 216 +P+++R + +W +F APA P+ ++ +RG+YL EG HC +CHTPRG Sbjct: 151 TWPLSMRWPLSIWRKVF------APAVAVDGPEDNSPLVRGQYLVEGLGHCGACHTPRGV 204 Query: 217 LMQEK-----TNLALSGAQVGPWYAPNITPHPTAGIGTWSQDELVAYLKTGRVEGRAQAA 271 MQEK ++ LSG + + A N+ G+G WS+ ++VA+LKTGR + A Sbjct: 205 GMQEKALSNDSSQFLSGGVIDGYLANNLRGDGRDGLGNWSEADIVAFLKTGR-NSHSAAF 263 Query: 272 GSMAEAITHSFSKLTDEDLRAIAVYLKE-------TPAIGPDSSTPPTLGTRFEQGKAGN 324 G MA+ + +S +T+EDL A+A YLK TPA+ D T L Sbjct: 264 GGMADVVANSTQYMTEEDLSAMAKYLKSLKPVKDGTPALAYDDKTHQAL----------- 312 Query: 325 ALAQFRGRTLAADSPEEIRGARLFSASCASCHGYNGQGTRDGYYPSLFHNSATAGVNANN 384 R + SP GA F +CA+CH +G+G D +PSL + N + Sbjct: 313 -------RKGSDQSP----GAMAFLNNCAACHRSSGKG-YDETFPSLALSPTVNAENPAS 360 Query: 385 LIATILYGVERE-TEDGGHVF-MPPFGDQPNALNKLSNEDVAALSNYLLKYYGNPDLKVK 442 LI +L G E T F MP FG ++LS+++VA + ++ +GN V Sbjct: 361 LIRIVLEGAEMPWTHKAPTQFAMPAFG------SRLSDQEVAEVVTFIRSSWGNQASSVS 414 Query: 443 PEDVAVIRQGGPR 455 DVA +R+ P Sbjct: 415 ASDVAKVRKQLPE 427 >gi|300313762|ref|YP_003777854.1| cytochrome c precursor protein [Herbaspirillum seropedicae SmR1] Length = 482 Score = 247 bits (630), Expect = 2e-66, Method: Compositional matrix adjust. Identities = 159/422 (37%), Positives = 219/422 (51%), Gaps = 34/422 (8%) Query: 40 AVSPEAALIERGRYLAVASDCIACHTAPRGKPMAGGLAIASPVGEIIATNITPSKSHGIG 99 + S E I RG YLA A DC+ACHT+ G P AGGLA+ASP+G I +TNITP K HGIG Sbjct: 75 SASAEDQQILRGAYLARAGDCVACHTSKGGAPFAGGLALASPIGAIYSTNITPDKQHGIG 134 Query: 100 NYSEAQFAAALRRGVRADGANLYPAMPYTAYAALNDADVHALYAYFMKGVAPVDTPTRET 159 ++S FA +R GV G +YPAMPY +Y+ L D D+ ALYAYF K V P R Sbjct: 135 DWSYEDFARLMRTGVTKAGYTVYPAMPYPSYSRLTDEDMQALYAYFSKAVPPSAQENRAN 194 Query: 160 ALPFPMNIRASMKVWNALFLKD-QPLAPAPQRSAQWLRGRYLAEGPAHCSSCHTPRGFLM 218 +P+P+++R + +W +F P PA + RG YL EG HC SCH+PR M Sbjct: 195 DIPWPLSMRWPLALWRKVFAPTPAPYTPAAGSDQELARGAYLVEGLGHCGSCHSPRAVTM 254 Query: 219 QEKT------NLALSGAQ-VGPWYAPNITPHPTAGIGTWSQDELVAYLKTGRVEGRAQAA 271 QEK L LSG Q V W P++ GI WSQ +LV +L+TGR + A + Sbjct: 255 QEKALKEDGGRLFLSGGQVVDGWSVPSLRNEHGGGIAGWSQADLVEFLRTGRNQYTA-SF 313 Query: 272 GSMAEAITHSFSKLTDEDLRAIAVYLKETPAIGPDSSTPPTLGTRFEQGKAGNALAQFRG 331 G+M + I S ++D DL A+A YL P P P R++ + A A + G Sbjct: 314 GAMNDVIEDSMQYMSDADLNAMARYLLSLP---PRQQAAP---YRYD---SATAQAAYDG 364 Query: 332 RTLAADSPEEIRGARLFSASCASCHGYNGQGTRDGYYPSLFHNSATAGVNANNLIATILY 391 R D P GAR++ CA+CH NG G +P+L N +A + I IL Sbjct: 365 RP---DGP----GARIYLDRCAACHRSNGTGYGKA-FPALAGNPVLQTSDATSAIRIILQ 416 Query: 392 GVERETEDGGH--VFMPPFGDQPNALNKLSNEDVAALSNYLLKYYGNPDLKVKPEDVAVI 449 G + + + M P+ L ++ VA +++Y+ +GN +VA + Sbjct: 417 GGRQPSTASATAGLVMAPYA------QLLDDQQVAEVTSYIQTAWGNRGGTTTAAEVAKV 470 Query: 450 RQ 451 R+ Sbjct: 471 RK 472 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.317 0.133 0.400 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,518,876 Number of extensions: 68432 Number of successful extensions: 254 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 210 Number of HSP's successfully gapped: 7 Length of query: 497 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 408 Effective length of database: 1,198,455 Effective search space: 488969640 Effective search space used: 488969640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 132 (55.5 bits)